COUNT 2.41 (DOS)
OBJECTIVES
This program was created to assist in the enumeration of
differentially repetitive items and to maintain the integrity
of data transfer between the physical count and data manipulation.
The experienced user of this program will find that the time
spent counting samples is greatly reduced compared to the
traditional methods of tally bars or pencil tics. Once becoming
touch sensitive with the 10-keypad, the user will be able to
maintain continuous eye contact with the sample, reducing the
time spent moving and refocussing their eyes. The risk of
loosing track of what was or was not counted is also
substantially reduced. The time spent on data transfer is
essentially reduced to zero as the output from this program
is directly importable to any major brand of spreadsheet
(i.e. Excel). Furthermore, this importability
reduces transfer error rates to zero.
GENERAL INFORMATION
This program has been created using the True Basic (Kemeny
and Kurtz) programming language. It has been compiled and
bound into a free-standing application that needs no other
software support. Files to be edited must be opened from
within another application (i.e. spreadsheet). These files
must be saved as an tab delimited ASCII text file.
The program uses a master file containing taxon names as row
titles, sample names as column titles, and their associated
counts. This format is common for data spreadsheets. The
program assigns each taxon a numeric integer equivalent.
This integer is entered on the computer keyboard and used
to score and record the numbers of a taxon observed in a sample.
The samples are referenced by their names. The program is also
capable of tracking two levels of area observed, for instance the
number of random microscopic fields observed and the number of
transects across a microscope slide observed. The initial master
file for a batch of samples must be created as a tab delimited
spreadsheet and saved as ASCII text. The master file is then
called, manipulated, and saved from within the counting program
until the batch is complete. The program also creates a small
backup file for each individual sample containing only counts
without taxon names.
The count program calculates a Shannon Diversity Index* (H')
on demand, when the master file is saved, or when the program
is exited. The maximum possible diversity value (Hmax) is also
calculated as is species eveness (J'). A small rudimentary
graph of change in diversity value is displayed after a sample's
second diversity calculation during a particular session.
*sum(pi log2 pi), where pi = ni/N
THE MASTER FILE
When creating a master file for a batch of samples, space for
more taxa than are known or are anticipated should be allocated.
This will accomodate unknown or new taxa found in the samples.
The extra allocations must have some "generic" code assigned to
them, i.e A, B, C, D. Six extra lines for summary information
should be included after your last taxon (see APPENDIX I). Each
non-sample name or taxon name cell should be filled with a 0
(zero) before you begin your first count. Once created,
"generic" rows can be assigned a proper name in the master
file from within a spreadsheet application. Once opened by
another application, the file must be saved as an ASCII text file.
See APPENDIX I for an example of the master file in spreadsheet
form. The program reads the first line of the master file (i.e.
50.25) to tell it how many taxa and samples are in the file.
In this case there will be 50 taxa and 25 samples. It is
important to note that these two numbers be separated by a '.'
(period). You can add more taxa or samples by using your
spreadsheet program, but be sure to change the appropriate
number in the header. Its been reported that Lotus 123 does not
write a text file format that my program can use.
GETTING STARTED
The first question the program will ask is to name the file to
open. Do so and the program will load it into memory. You will
then be prompted to define a multiple unit key. This key will
alow you to enter multiple units of a particular taxon. This
non-numeric key should the one nearest the enter key associated
with the 10-key portion of your keyboard. You'll also be asked
to hit your 'tab' key. This is because the numeric code for that
key is different on different PC clones.
COUNTING
You will be presented with an on screen menu of your sample
names (the program can accommodate 70 samples in a batch).
Point and click on the box associated with the sample you wish
to count. The program loads the sample and displays pertinent
information about that sample, including; the number of declared
taxa available, the total number of cells counted to date, the
number of fields counted, the number of strips counted, the
master file name (if any is given at this point), and the
sample name.
You should have a hard copy reference list of all taxon numbers
and their assigned name, either specific or "generic" before you
begin counting. When you assign specific names to "generic"
taxon numbers you can record them on this reference list.
SINGLE ENTRY OPTION:
A taxon is enumerated by entering the number associated with
that taxon and will increase the cumulative count for the taxon
by one unit. If you attempt to enter a positive integer greater
than your last allocated taxon number you will be warned with
a unique sound and asked to reenter a taxon number within the
allocated range. A similar result occurs if you attempt to
enter a fractional taxon number, i.e. 12.6 or 0.3. Upon
successfully scoring one taxon number you will hear one short
beep. The pitch of that beep is unique for that taxon. The
program then displays the taxon name scored, the taxon number,
the cumulative count for that taxon, and the cumulative count
for all taxa. If you have a field of view containing a filament,
a colony, or multiple cells of one taxon, you can score multiple
units of one taxon by hitting the key you defined as the multiple
unit key above within 0.25 seconds of entering the taxon number.
Entering the taxon number scores the first unit of the group, you
then enter the number of additional units you wish to score and
are returned to the 'Enter the Taxon Number to Score' prompt.
You may also subtract through this subroutine by preceeding the
number of units with a '-' sign (remember to subtract one
addtional unit to account for the first unit scored to get you
into the subroutine) as well as enter fractional units.
SUBTRACTION:
Immediately after scoring one unit of a taxon you may subtract
that unit by entering '0' (zero). It may be that you changed
your identification of that unit or miskeyed the entry number.
After you have scored the next taxon the '0' subtraction option
applies to the new taxon.
SCORING FIELDS OF VIEW:
Any negative number, except '-1' and '-11', will add one field
of view to the cumulative total of fields.
SCORING STRIPS OF VIEW:
By entering '-1' you will add one strip of view to the cumulative
total of strips. Entering '-11' subtracts one strip.
OPTIONS MENU:
When you enter '999' the program displays an on screen options
menu. At this point you may calculate a Shannon Diversity Index,
save your work, start a new count, save your work and quit the
program, or exit the options menu back to the current count.
When you save your work you will be prompted to enter a file name.
If this is the initial save for the master file you should entitle
it at this time, or else overwrite the old master file. If you
suspect you have input some kind of erroneous information during
the current count, change the title and save. The old master file,
prior to the current count, will remain intact and you can exit
the program and redo the current count using the untouched old
master file. The program creates a small backup file for that
sample in addition to updating the master file whenever you save
your data, start a new count, or quit the program. This file
will be titled by the sample name, it will not contain taxon
names, but rather contain the count for each taxon in order.
Additionally, the total units, fields, strips, and diversity
information are included in the backup file.
DATA TRANSFER
When all samples in a master file are completed the data are
ready to be transferred to a spreadsheet application. To
transfer the data, open the spreadsheet application, define
tab delimitation (if necessary) to the application, and open
the master file into the spreadsheet. The data should then be
manipulatible to your needs.
ADDITIONAL INFO
Should you run out of allocated taxa space before a batch of
samples are complete you may add taxa directly to the master
file by opening it from within a spreadsheet application. Then
insert and name as many taxa rows as you feel you need, enter a
0, return to the top line of the file and change the number before
the '.' to reflect the number of additional taxa, and save the file
as an ASCII text file.
Several 'run time errors' may occur, particularly when opening
the master file after some external modification. These may
include; "Too many input items", "Too few input items", "Reading
past the end of the file", or "File is the wrong type". Check to
insure the additional lines are formatted properly, that you
have entered a 0 for every sample, that you have changed the first
number in the top line of the file, and that the file is saved as
ASCII text. If a problem occurs while loading a sample or taxon
names file, check to insure that each item is on its own line,
and that a carriage return follows the last character of the line,
except the last line of the file.
Although I have diligently attempted to protect this program and
your data from miskeys and illegal entries, I am human and may
not have anticipated some scenarios. I therefore cannot be
responsible for lost data. To make any data loss minimal, I
suggest you make a duplicate of the master file (throwing away
the old duplicate) after every couple of samples. If you somehow
destroy the master file from within the counting program I would
appreciate knowing about it and how it happened so that I can
correct the problem for you and future users. I would also
appreciate receiving general ideas as to how the program might
be improved. Please feel free to contact me for any reason.
David W. Johnson
Dept. of Biological Sciences
BGSU
Bowling Green, OH 43403
LAB (419)372-8562
FAX (419)372-2024
e-MAIL djohnso@opie.bgsu.edu
APPENDIX I
SAMPLE MASTER FILE (as viewed using EXCEL)
20.9
DARBY1 C1 C2 C3 N1 N2 N3 P1 P2 P3
Achnanthes 0 0 0 0 0 0 0 0 0
Amphora 0 0 0 0 0 0 0 0 0
Cocconeis 0 0 0 0 0 0 0 0 0
Gompho 0 0 0 0 0 0 0 0 0
Fragilaria 0 0 0 0 0 0 0 0 0
Hantzschia 0 0 0 0 0 0 0 0 0
Melosira 0 0 0 0 0 0 0 0 0
Navicula1 0 0 0 0 0 0 0 0 0
Navicula2 0 0 0 0 0 0 0 0 0
Nitzschia1 0 0 0 0 0 0 0 0 0
Nitzschia2 0 0 0 0 0 0 0 0 0
Rhoico 0 0 0 0 0 0 0 0 0
Surirella 0 0 0 0 0 0 0 0 0
AA 0 0 0 0 0 0 0 0 0
BB 0 0 0 0 0 0 0 0 0
CC 0 0 0 0 0 0 0 0 0
DD 0 0 0 0 0 0 0 0 0
EE 0 0 0 0 0 0 0 0 0
FF 0 0 0 0 0 0 0 0 0
GG 0 0 0 0 0 0 0 0 0
TOT UNITS 0 0 0 0 0 0 0 0 0
# of FIELDS 0 0 0 0 0 0 0 0 0
# of STRIPS 0 0 0 0 0 0 0 0 0
H' 0 0 0 0 0 0 0 0 0
Hmax 0 0 0 0 0 0 0 0 0
J' 0 0 0 0 0 0 0 0 0
APPENDIX II
NUMERIC ENTRIES for THE COUNTING PROGRAM
1) Any integer between 1 and your last allocated taxa number,
inclusive, scores one unit to that taxon number.
2) Zero (0) subtracts one unit from the taxon just scored.
3) -1 adds one strip.
4) -11 subtracts one strip
5) Any negative integer except -1, -11, and -999 scores one
field of view.
6) 999 displays the options menu
a) Calculate a Shannon Diversity Index
b) Save your work
c) Start a new count
d) Quit the program
e) Exit the options menu (return to your current count)